From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 15 Dec 2004 17:15:25 +0000 (+0000)
Subject: REpainting after graph panel setVisible fixed
X-Git-Tag: Release_2_0~817
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c36a5cbdcbb1c099320e1454c1038327efa04efa;p=jalview.git

REpainting after graph panel setVisible fixed
---

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index fcb5a57..bc6ea86 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -75,8 +75,11 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   public void setGraphPanelVisible(boolean b)
   {
-    scorePanelHolder.setVisible(b);
     idSpaceFillerPanel.setVisible(b);
+    scorePanelHolder.setVisible(b);
+
+    RefreshPanels();
+    // bit annoying to call this twice, can you do better?
     RefreshPanels();
   }
 
@@ -113,168 +116,21 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     seqPanel.seqCanvas.paintFlag = true;
     repaint();
   }
-  /*
-    seqCanvas.paintFlag = true;
-    if (av.getSelection().size() == 0)
-    {
-      seqCanvas.globalColorScheme = cs;
-      for (int i = 0; i < av.alignment.getGroups().size();i++)
-      {
-        SequenceGroup sg = (SequenceGroup)av.alignment.getGroups().elementAt(i);
-        sg.cs = cs;
-        if(!showConservation
-            && !(sg.cs instanceof Blosum62ColourScheme)
-            && sg.cs instanceof ConservationColourScheme)
-         {
-           // remove ConservationColouring from existing Conservation group
-           ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-           sg.cs = ccs.cs;
-         }
-         else if(showConservation && !(sg.cs instanceof ConservationColourScheme))
-         {
-           // add ConservationColouring to new group
-           Conservation c = sg.getConservation();
-           Alignment al = (Alignment) av.getAlignment();
-           c = new Conservation("All", al.cons,
-                                ResidueProperties.propHash, 3, sg.sequences, 0,
-                                al.getWidth() );
-           c.calculate();
-           c.verdict(false, 100);
-           sg.setConservation(c);
-           sg.cs = new ConservationColourScheme(sg);
-         }
-      }
-    }
-    else
-    {
-      SequenceGroup sg = av.alignment.findGroup((Sequence)av.sel.sequenceAt(0));
-
-      if( isNewSelection(sg) )
-      {
-        sg = av.getAlignment().addGroup();
-        for (int i=0; i < av.getSelection().size(); i++)
-        {
-          av.alignment.removeFromGroup(av.alignment.findGroup( (Sequence) av.
-              sel.sequenceAt(i)),
-                                       (Sequence) av.sel.sequenceAt(i));
-          av.alignment.addToGroup(sg, (Sequence) av.sel.sequenceAt(i));
-        }
-      }
-
-
-      sg.cs = cs;
-
-      // Selection is made, we only want to change the conservationColour for selected group
-      if(  showConservation
-           && !(sg.cs instanceof ConservationColourScheme)
-           && !(sg.cs instanceof Blosum62ColourScheme))
-      {
-        Conservation c = sg.getConservation();
-        Alignment al = (Alignment) av.getAlignment();
-
-        c = new Conservation("All", al.cons,
-                             ResidueProperties.propHash, 3, sg.sequences, 0,
-                             al.getWidth() );
-        c.calculate();
-        c.verdict(false, 100);
-        sg.setConservation(c);
-        sg.cs = new ConservationColourScheme(sg);
-    }
-    else  if( !showConservation && sg.cs instanceof ConservationColourScheme)
-    {
-      ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-      sg.cs = ccs.cs;
-    }
-   }
-   repaint();
-  }
-
-  boolean isNewSelection(SequenceGroup sg)
-  {
-    if(sg==null)
-      return true;
-
-    if(sg.getSize()!=av.getSelection().size())
-      return true;
-
-    for(int i=0; i<sg.getSize(); i++)
-     if( !av.getSelection().contains( sg.getSequenceAt(i) ))
-       return true;
-
-    return false;
-  }
-
-
-  public ColourSchemeI getColourScheme()
-  {
-    if(av.getSelection().size()>0)
-       return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs;
-    else
-      return seqCanvas.globalColorScheme;
-  }
-*/
-
-/*  public void setColourScheme(jalview.schemes.ColourSchemeI cs, boolean conservation)
-  {
-    seqPanel.setColourScheme(cs, conservation);
-
-    av.setGlobalColourScheme(cs);
-
-    if(overviewPanel!=null)
-      overviewPanel.updateOverviewImage();
-  }
-
-   void updateResidueView()
-   {
-     if (viewport.getSelection().size() == 0)
-      {
-        for (int i = 0; i < viewport.alignment.getGroups().size(); i++)
-        {
-          SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i);
-          sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() );
-          sg.setDisplayText( viewTextMenuItem.isSelected() );
-          sg.setColourText( colourTextMenuItem.isSelected() );
-        }
-      }
-      else
-      {
-        SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0));
-        if (alignPanel.seqPanel.isNewSelection(sg))
-        {
-          sg = viewport.getAlignment().addGroup();
-          for (int i = 0; i < viewport.getSelection().size(); i++)
-          {
-            viewport.alignment.removeFromGroup(viewport.alignment.findGroup( (
-                Sequence) viewport.sel.sequenceAt(i)),
-                                               (Sequence) viewport.sel.sequenceAt(
-                i));
-            viewport.alignment.addToGroup(sg,
-                                          (Sequence) viewport.sel.sequenceAt(i));
-          }
-        }
-
-        sg.setDisplayBoxes(viewBoxesMenuItem.isSelected());
-        sg.setDisplayText(viewTextMenuItem.isSelected());
-        sg.setColourText(colourTextMenuItem.isSelected());
-      }
-     alignPanel.RefreshPanels();
-   }*/
-
-
 
   public void RefreshPanels()
   {
+
     invalidate();
     seqPanel.seqCanvas.paintFlag = true;
     idPanel.idCanvas.paintFlag = true;
     idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
     setScrollValues(av.getStartRes(), av.getStartSeq());
     av.getConsensus(true);
-    validate();
-    repaint();
     if(overviewPanel!=null)
       overviewPanel.updateOverviewImage();
 
+    validate();
+    repaint();
   }
 
   int hextent = 0;
@@ -299,6 +155,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
     vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
+
+
     repaint();
 
   }